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Ly LC, Yang Y, Li F, Crossley M, Shi Y, Quinlan KGR. Protocols for protein-DNA binding analysis of a zinc finger transcription factor bound to its cognate promoter. STAR Protoc 2022; 3:101598. [PMID: 35928006 PMCID: PMC9344028 DOI: 10.1016/j.xpro.2022.101598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Yang Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yunyu Shi
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China.
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end. Mol Cell 2021; 81:4271-4286.e4. [PMID: 34403695 DOI: 10.1016/j.molcel.2021.07.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022]
Abstract
Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Although most eukaryotic transposases form oligomers and use RNase H-like domains to break and rejoin double-stranded DNA (dsDNA), Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain. Here, we report the cryo-electron microscopy structure of a Helitron transposase bound to the 5'-transposon end, providing insight into its multidomain architecture and function. The monomeric transposase forms a tightly packed assembly that buries the covalently attached cleaved end, protecting it until the second end becomes available. The structure reveals unexpected architectural similarity to TraI, a bacterial relaxase that also catalyzes ssDNA movement. The HUH active site suggests how two juxtaposed tyrosines, a feature of many replication initiators that use HUH nucleases, couple the conformational shift of an α-helix to control strand cleavage and ligation reactions.
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Liu L, Wang Y, Li Y, Ding C, Zhao P, Xia Q, He H. Cross-talk between juvenile hormone and ecdysone regulates transcription of fibroin modulator binding protein-1 in Bombyx mori. Int J Biol Macromol 2019; 128:28-39. [PMID: 30682471 DOI: 10.1016/j.ijbiomac.2019.01.092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 01/05/2023]
Abstract
Juvenile hormone (JH) and 20-hydroxyecdysone (20E) are the most important hormones in silkworm and play vital roles in silkworm development, metamorphosis, and silk protein synthesis. Fibroin modulator binding protein-1 (FMBP-1) is a novel transcription factor regulating fibroin heavy chain (fib-H) transcription in Bombyx mori. The roles of JH and 20E on FMBP-1 transcription are less known. Here, we show FMBP-1 transcription is repressed by juvenile hormone analog (JHA) and activated by 20E. We identify two Krüppel homolog 1 (Kr-h1) binding sites (KBS1 and KBS2) and an E74A binding site (EBS) in the promoter of FMBP-1. We demonstrate Kr-h1 directly binds to KBS1 and KBS2 to repress FMBP-1 transcription, and 20E promotes FMBP-1 transcription through E74A. In the presence of JH and 20E, E74A abolishes the repression of Kr-h1 and activates FMBP-1 transcription through direct binding to EBS between KBS1 and KBS2 in FMBP-1 promoter. Further, JHA and 20E treatment and RNA interference confirm the effects of JH and 20E on FMBP-1 transcription in vivo, thus affecting fib-H transcription. Our results reveal the molecular mechanism of FMBP-1 transcription regulated by the cross-talk between JH and 20E in Bombyx mori, and provide novel insights into FMBP-1 transcriptional regulation and silk protein synthesis.
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Affiliation(s)
- Lina Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
| | - Yejing Wang
- College of Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
| | - Yu Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
| | - Chaoxiang Ding
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China
| | - Huawei He
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China.
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Liu L, Wang Y, Li Y, Guo P, Liu C, Li Z, Wang F, Zhao P, Xia Q, He H. Insights into the repression of fibroin modulator binding protein-1 on the transcription of fibroin H-chain during molting in Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 104:39-49. [PMID: 30543984 DOI: 10.1016/j.ibmb.2018.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Fibroin modulator binding protein-1 (FMBP-1) is a novel DNA-binding protein containing a conserved score and three amino acid peptide repeat (STPR) domain. The roles of factors containing STPR domain are less known. Although multiple transcription factors are involved in the transcriptional regulation of silk protein genes during the development of silkworm, the mechanism of transcriptional repression of silk protein genes during molting remains unclear. Here, we found that FMBP-1 expression was contrary to that of fibroin heavy chain (fib-H) during the fourth molting period of Bombyx mori. FMBP-1 repressed fib-H promoter activity by directly binding to the -130 element in the fib-H promoter region. We also identified two proteins, Bmsage and Bmdimm, that interacted with FMBP-1 in the posterior silk gland of silkworm larvae, and further verified these interactions by far western blotting and microscale thermophoresis in vitro, as well as co-immunoprecipitation and bimolecular fluorescence complementation at the cellular level. The luciferase reporter assay showed that the interaction between FMBP-1 and Bmdimm antagonized the activation of Bmdimm on fib-H transcription, but did not affect FMBP-1-mediated transcriptional repression on fib-H gene. Therefore, we proposed the following mechanism of fib-H transcriptional repression by FMBP-1 during the molting of silkworm larvae: 1) FMBP-1 directly binds to the -130 element in the fib-H promoter to repress fib-H transcription; 2) FMBP-1 interacts with Bmdimm to antagonize the activation of Bmdimm on fib-H transcription. Our findings promote a better understanding of fib-H transcriptional regulation and provide novel insights into the transcriptional repression of fib-H by FMBP-1 and basic helix-loop-helix factors Bmdimm during the molting of silkworm larvae. Our study also provides valuable information regarding the biological function of factors containing STPR domain.
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Affiliation(s)
- Lina Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Yejing Wang
- College of Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
| | - Yu Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Pengchao Guo
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Chun Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Zhiqing Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Feng Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing, 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing, 400715, China.
| | - Huawei He
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing, 400715, China.
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